forked from D-Net/dnet-hadoop
[patents] added test and resources
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@ -37,7 +37,8 @@ public class PrepareResultCommunitySetStep1 {
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* relation
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*/
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// TODO
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private static final String RESULT_CONTEXT_QUERY_TEMPLATE = "select target resultId, community_context "
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private static final String RESULT_CONTEXT_QUERY_TEMPLATE =
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"select target resultId, community_context "
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+ "from (select id, collect_set(co.id) community_context "
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+ " from result "
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+ " lateral view explode (context) c as co "
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@ -59,15 +60,26 @@ public class PrepareResultCommunitySetStep1 {
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+ "where length(co) > 0 "
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+ "group by resultId";
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private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO = "select target resultId, community_context "
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+ "from (select id, collect_set(co.id) community_context "
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+ " from result "
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+ " lateral view explode (context) c as co "
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+ " where datainfo.deletedbyinference = false %s "
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+ " and array_contains(instance.instancetype.classname, 'Patent') group by id) p "
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+ " JOIN "
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+ " (select source, target from relation "
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+ " where datainfo.deletedbyinference = false %s ) r ON p.id = r.source";
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private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO =
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"select target as resultId, community_context " +
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"from resultWithContext rwc " +
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"join relatedToRelations r " +
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"join patents p " +
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"on rwc.id = r.source and r.target = p.id";
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private static final String RESULT_WITH_CONTEXT = "select id, collect_set(co.id) community_context \n" +
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" from result " +
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" lateral view explode (context) c as co " +
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" where datainfo.deletedbyinference = false AND lower(co.id) IN %s" +
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" group by id";
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private static final String RESULT_PATENT = "select id " +
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" from result " +
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" where array_contains(instance.instancetype.classname, 'Patent')";
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private static final String IS_RELATED_TO_RELATIONS = "select source, target " +
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" from relation " +
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" where lower(relClass) = 'isrelatedto' and datainfo.deletedbyinference = false";
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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@ -95,20 +107,18 @@ public class PrepareResultCommunitySetStep1 {
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";"))
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.map(value -> "'" + value.toLowerCase() + "'")
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.toArray(String[]::new));
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log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
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final String allowedsemrel ="(" + join(",",
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Arrays.asList(parser.get("allowedsemrels").split(";")).stream().map(value -> "'" + value.toLowerCase() + "'")
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.toArray(String[]::new)) + ")";
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log.info("allowedSemRel: {}", allowedsemrel);
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final String baseURL = parser.get("baseURL");
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log.info("baseURL: {}", baseURL);
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final String communityIdList = join(",", getCommunityList(baseURL).stream()
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final String communityIdList = "(" + join(",", getCommunityList(baseURL).stream()
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.map(value -> "'" + value.toLowerCase() + "'")
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.toArray(String[]::new));
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.toArray(String[]::new)) + ")";
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log.info("communityIdList: {}", new Gson().toJson(communityIdList));
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final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
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log.info("resultType: {}", resultType);
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@ -156,32 +166,38 @@ public class PrepareResultCommunitySetStep1 {
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final String outputResultPath = outputPath + "/" + resultType;
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log.info("writing output results to: {}", outputResultPath);
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String resultContextQuery = String
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.format(
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RESULT_CONTEXT_QUERY_TEMPLATE,
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" lower(co.id) IN " + communityIdList,
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" AND lower(relClass) IN " + allowedsemrel);
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String resultContextQueryIsRelatedTo = String
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.format(
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RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO,
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" AND lower(co.id) IN " + communityIdList,
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"AND lower(relClass) = '"+
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ModelConstants.IS_RELATED_TO.toLowerCase() + "'");
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"AND lower(co.id) IN " + communityIdList,
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"AND lower(relClass) IN " + allowedsemrel);
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Dataset<Row> result_context = spark.sql(resultContextQuery);
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//result_context.createOrReplaceTempView("result_context");
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// spark
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// .sql(RESULT_COMMUNITY_LIST_QUERY)
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// .as(Encoders.bean(ResultCommunityList.class))
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// .write()
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// .option("compression", "gzip")
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// .mode(SaveMode.Overwrite)
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// .json(outputResultPath);
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Dataset<Row> rwc = spark.sql(String.format(RESULT_WITH_CONTEXT, communityIdList));
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Dataset<Row> patents = spark.sql(RESULT_PATENT);
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Dataset<Row> relatedToRelations = spark.sql(IS_RELATED_TO_RELATIONS);
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rwc.createOrReplaceTempView("resultWithContext");
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patents.createOrReplaceTempView("patents");
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relatedToRelations.createOrReplaceTempView("relatedTorelations");
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result_context = result_context.unionAll( spark.sql(RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO));
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result_context.createOrReplaceTempView("result_context");
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spark
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.sql(RESULT_COMMUNITY_LIST_QUERY)
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.as(Encoders.bean(ResultCommunityList.class))
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Overwrite)
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.json(outputResultPath);
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result_context = spark.sql(resultContextQueryIsRelatedTo);
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result_context.createOrReplaceTempView("result_context");
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spark
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.sql(RESULT_COMMUNITY_LIST_QUERY)
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.as(Encoders.bean(ResultCommunityList.class))
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@ -189,6 +205,7 @@ public class PrepareResultCommunitySetStep1 {
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.option("compression", "gzip")
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.mode(SaveMode.Append)
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.json(outputResultPath);
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}
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public static List<String> getCommunityList(final String baseURL) throws IOException {
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@ -6,8 +6,11 @@ import static org.apache.spark.sql.functions.desc;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.stream.Collectors;
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import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
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import org.apache.commons.io.FileUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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@ -25,6 +28,7 @@ import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.oaf.Dataset;
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import scala.collection.Seq;
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public class ResultToCommunityJobTest {
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@ -271,4 +275,55 @@ public class ResultToCommunityJobTest {
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.get(0)
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.getString(0));
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}
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@Test
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public void prepareStep1Test() throws Exception {
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/*
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final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";"))
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.map(value -> "'" + value.toLowerCase() + "'")
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.toArray(String[]::new));
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log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
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final String baseURL = parser.get("baseURL");
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log.info("baseURL: {}", baseURL);
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*/
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PrepareResultCommunitySetStep1
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-sourcePath", getClass()
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.getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph")
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.getPath(),
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"-hive_metastore_uris", "",
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-outputPath", workingDir.toString() + "/preparedInfo",
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"-allowedsemrels","issupplementto;issupplementedby",
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"-baseURL","https://dev-openaire.d4science.org/openaire/community/"
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});
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org.apache.spark.sql.Dataset<ResultCommunityList> resultCommunityList = spark.read().schema(Encoders.bean(ResultCommunityList.class).schema())
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.json(workingDir.toString() + "/preparedInfo/publication")
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.as(Encoders.bean(ResultCommunityList.class));
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Assertions.assertEquals(2, resultCommunityList.count());
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Assertions.assertEquals(1,resultCommunityList.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'").count());
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Assertions.assertEquals(1,resultCommunityList.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'").count());
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ArrayList<String> communities = resultCommunityList
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.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'")
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.first().getCommunityList();
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Assertions.assertEquals(2, communities.size());
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Assertions.assertTrue(communities.stream().anyMatch(cid -> "beopen".equals(cid)));
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Assertions.assertTrue(communities.stream().anyMatch(cid -> "dh-ch".equals(cid)));
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communities = resultCommunityList
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.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'")
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.first().getCommunityList();
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Assertions.assertEquals(1, communities.size());
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Assertions.assertEquals("dh-ch", communities.get(0));
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}
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}
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File diff suppressed because one or more lines are too long
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@ -0,0 +1,24 @@
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"issupplementedby","relType":"resultOrganization","source":"50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6","subRelType":"affiliation","target":"50|pending_org_::82f63b2d21ae88596b9d8991780e9888","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"issupplementedby","relType":"resultOrganization","source":"50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6","subRelType":"affiliation","target":"50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"IsProvidedBy","relType":"resultOrganization","source":"10|opendoar____::f0dd4a99fba6075a9494772b58f95280","subRelType":"affiliation","target":"20|openorgs____::322ff2a6524820640bc5d1311871585e","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"IsProvidedBy","relType":"resultOrganization","source":"10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539","subRelType":"affiliation","target":"20|openorgs____::58e60f1715d219aa6757ba0b0f2ccbce","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"IsProvidedBy","relType":"resultOrganization","target":"20|openorgs____::64badd35233ba2cd4946368ef2f4cf57","subRelType":"affiliation","source":"10|issn___print::a7a2010e75d849442790955162ef4e42","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"IsProvidedBy","relType":"resultOrganization","source":"10|issn___print::a7a2010e75d849442790955162ef4e43","subRelType":"affiliation","target":"20|openorgs____::64badd35233ba2cd4946368ef2f4cf57","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"IsProvidedBy","relType":"resultOrganization","source":"10|issn___print::a7a2010e75d849442790955162ef4e44","subRelType":"affiliation","target":"20|openorgs____::548cbb0c5a93722f3a9aa62aa17a1ba1","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"IsProvidedBy","relType":"resultOrganization","source":"10|issn___print::a7a2010e75d849442790955162ef4e45","subRelType":"affiliation","target":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isrelatedto","relType":"resultOrganization","source":"50|openorgs____::64badd35233ba2cd4946368ef2f4cf57","subRelType":"affiliation","target":"50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783","subRelType":"affiliation","target":"20|openorgs____::64badd35233ba2cd4946368ef2f4cf57","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isrelatedto","relType":"resultOrganization","source":"50|355e65625b88::74009c567c81b4aa55c813db658734df","subRelType":"affiliation","target":"50|dedup_wf_001::08d6f2001319c86d0e69b0f83ad75df2","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::08d6f2001319c86d0e69b0f83ad75df2","subRelType":"affiliation","target":"20|openorgs____::91a81877815afb4ebf25c1a3f3b03c5d","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|openorgs____::548cbb0c5a93722f3a9aa62aa17a1ba1","subRelType":"affiliation","target":"50|dedup_wf_001::0a1cdf269375d32ce341fdeb0e92dfa8","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0a1cdf269375d32ce341fdeb0e92dfa8","subRelType":"affiliation","target":"20|openorgs____::548cbb0c5a93722f3a9aa62aa17a1ba1","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|pending_org_::a50fdd7f7e77b74ea2b16823151c391a","subRelType":"affiliation","target":"50|dedup_wf_001::0ab92bed024ee6883c7a1244722e5eec","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0ab92bed024ee6883c7a1244722e5eec","subRelType":"affiliation","target":"20|pending_org_::a50fdd7f7e77b74ea2b16823151c391a","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|openorgs____::64badd35233ba2cd4946368ef2f4cf57","subRelType":"affiliation","target":"50|dedup_wf_001::0ca26c736ad4d15b3d5ee90a4d7853e1","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0ca26c736ad4d15b3d5ee90a4d7853e1","subRelType":"affiliation","target":"20|openorgs____::64badd35233ba2cd4946368ef2f4cf57","validated":false}
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|pending_org_::a50fdd7f7e77b74ea2b16823151c391a","subRelType":"affiliation","target":"50|dedup_wf_001::0ef8dfab3927cb4d69df0d3113f05a42","validated":false}
|
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0ef8dfab3927cb4d69df0d3113f05a42","subRelType":"affiliation","target":"20|pending_org_::a50fdd7f7e77b74ea2b16823151c391a","validated":false}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|openorgs____::548cbb0c5a93722f3a9aa62aa17a1ba1","subRelType":"affiliation","target":"50|dedup_wf_001::0f488ad00253126c14a21abe6b2d406c","validated":false}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0f488ad00253126c14a21abe6b2d406c","subRelType":"affiliation","target":"20|openorgs____::548cbb0c5a93722f3a9aa62aa17a1ba1","validated":false}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","subRelType":"affiliation","target":"50|dedup_wf_001::12206bf78aabd7d52132477182d19147","validated":false}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::12206bf78aabd7d52132477182d19147","subRelType":"affiliation","target":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","validated":false}
|
||||
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Reference in New Issue